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TypeError exception when importing a packed workflow #91

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ghost opened this issue Dec 27, 2018 · 0 comments
Open

TypeError exception when importing a packed workflow #91

ghost opened this issue Dec 27, 2018 · 0 comments

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@ghost
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ghost commented Dec 27, 2018

Workflow is packed with command below:

$ cwltool --pack cmsearch-multimodel-wf.cwl > cmsearch-multimodel-wf-packed.cwl

When importing the packed workflow in Galaxy, exception below occurs:

Traceback (most recent call last):
  File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "lib/galaxy/webapps/galaxy/api/workflows.py", line 337, in create
    return self.__api_import_from_archive(trans, archive_data, source="uploaded file", from_path=os.path.abspath(uploaded_file_name))
  File "lib/galaxy/webapps/galaxy/api/workflows.py", line 596, in __api_import_from_archive
    raw_workflow_description = self.__normalize_workflow(trans, data)
  File "lib/galaxy/webapps/galaxy/api/workflows.py", line 679, in __normalize_workflow
    return self.workflow_contents_manager.normalize_workflow_format(trans, as_dict)
  File "lib/galaxy/managers/workflows.py", line 315, in normalize_workflow_format
    workflow_path += "#" + object_id
TypeError: unsupported operand type(s) for +=: 'NoneType' and 'str'

Adding 'src' and 'path' attributes in 'data' dict prevents the exception.

e6a4d11
(galaxy fork)

@ghost ghost mentioned this issue Dec 27, 2018
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